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1,721
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1,721 results for “network data”
Data from: Hierarchical social networks shape gut microbial composition in wild Verreaux's sifaka
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Data from: Multiple stressors in river networks: Local and downstream effects on freshwater macroinvertebrates
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Data for: Induction of C4 genes during de-etiolation of Gynandropsis gynandra evolved through changes in cis allowing integration into ancestral C3 gene regulatory networks
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Data for: Brain control of bimanual movement enabled by recurrent neural networks
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Data from: Pleiotropy alleviates the fitness costs associated with resource allocation trade-offs in immune signaling networks
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Data from: Characterizing the hyperuniformity of disordered network metamaterials
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Data for: Social network data in wild great tits during ontogeny
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R_JAGS code for estimation and analysis of species-area-relationship (SAR) parameters from NEON (National Ecological Observatory Network) data on plant surveys
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Data for: Parameter selection and optimization of a computational network model of blood flow in single-ventricle patients
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Snow depth, air temperature, humidity, soil moisture and temperature, and solar radiation data from the basin-scale wireless-sensor network in American River Hydrologic Observatory (ARHO)
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Data from: A reusable pipeline for large-scale fiber segmentation on unidirectional fiber beds using fully convolutional neural networks
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Fish richness, density, and biomass data for a network of community-based no-take reserves in northern Thailand.
Intensive fisheries have reduced fish biodiversity and abundance in aquatic ecosystems worldwide. The widespread success of no-take reserves has made them a cornerstone of marine ecosystem-based fisheries management. A set of design principles has emerged to ensure that networks of marine reserves will enhance adjacent fisheries, but the applicability of this paradigm to riverine biodiversity and inland fisheries remains largely untested. Here we show that a diffuse set of 23 community-designated reserves in Thailand’s Salween basin has dramatically increased local fish richness, density, and biomass. We find that several key correlates of protected area success in marine ecosystems-particularly reserve size and enforcement-also predict differences in ecological benefits among riverine reserves. Moreover, occupying a central position in the network confers additional gains, underscoring the importance of connectivity within dendritic river systems. The emergence of network-based benefits is remarkable given that these reserves are young (< 25 years) and arose without formal coordination or spatial planning among communities. Freshwaters are under-represented among the world’s protected areas, and our findings suggest that networks of small reserves offer an effective and generalizable model for protecting biodiversity and augmenting fisheries as the world’s rivers face unprecedented pressures.
SOils DAta Harmonization database (SoDaH): an open-source synthesis of soil data from research networks
This SOils DAta Harmonization (SoDaH) database is designed to bring together soil carbon data from diverse research networks into a harmonized dataset that can be used for synthesis activities and model development. The research network sources for SoDaH span different biomes and climates, encompass multiple ecosystem types, and have collected data across a range of spatial, temporal, and depth gradients. The rich data sets assembled in SoDaH consist of observations from monitoring efforts and long-term ecological experiments. The SoDaH database also incorporates related environmental covariate data pertaining to climate, vegetation, soil chemistry, and soil physical properties. The data are harmonized and aggregated using open-source code that enables a scripted, repeatable approach for soil data synthesis.
temporalNEON: Repository containing raw and cleaned-up organismal data from the National Ecological Observatory Network (NEON) useful for evaluating the links between change in biodiversity and ecosystem stability
Organismal data include the following taxonomic groups: small mammals, fish, ground beetles, and aquatic macroinvertebrates. Data were retrieved from the National Ecological Observatory Network (NEON) database in November 2020. We submit both raw data retrieved from NEON as .rds files, R code used to process these data, as well as processed data as .csv files.
Sap Flux and Microclimate Data for Co-Occurring White Spruce and Paper Birch at an Intermediate Aged Stand in the Bonanza Creek LTER Regional Site Network 2013-2018
This dataset contains hourly mean sap flux density and microclimate data for co-occurring white spruce and Alaska paper birch from early June of 2013 to mid-September of 2018. The data were published as part of a 2021 article in Journal of Ecology.
Data of Bayesian inference of non-linear multiscale model parameters accelerated by a Deep Neural Network
<pre>Data from title = "Bayesian inference of non-linear multiscale model parameters accelerated by a Deep Neural Network", journal = "Computer Methods in Applied Mechanics and Engineering", pages = "112693", year = "2020", issn = "0045-7825", doi = "https://doi.org/10.1016/j.cma.2019.112693", author = "Wu, Ling and Zulueta, Kepa and Major, Zoltan and Arriaga, Aitor and Noels, Ludovic" </pre>
Code and data for: Network-based protein structural classification
<p>Code and data related to the research article titled, "Network-based protein structural classification".</p> <p>More information about the code and the data is available at https://nd.edu/~cone/NETPCLASS/</p>
Supplementary data for article 'Estimating and abstracting the 3D structure of feline bones using neural networks on X-ray (2D) images'
<p>3D DICOM volumes (CT scans) of feline femora, PNGs generated from them as DRRs using MeVisLab, and STLs generated from the DICOM volumes with MIMICS or MeshLab. Software to work with these files can be found at http://doi.org/10.5281/zenodo.3829423</p>
Data from: The functional roles of species in metacommunities, as revealed by metanetwork analyses of bird-plant frugivory networks
<p>Understanding how biodiversity and interaction networks change across environmental gradients is a major challenge in ecology. We integrated metacommunity and metanetwork perspectives to test species' functional roles in bird-plant frugivory interactions in a fragmented forest landscape in Southwest China, with consequences for seed dispersal. Availability of fruit resources both on and under trees created vertical feeding stratification for frugivorous birds. Bird-plant interactions involving birds feeding only on the tree or both on and under the tree (shared) had a higher centrality and contributed more to metanetwork organization than interactions involving birds feeding only under the tree. Moreover, bird-plant interactions associated with large-seeded plants disproportionately contributed to metanetwork organization and centrality. Consequently, on-the-tree and shared birds contributed more to metanetwork organization whereas under-the-tree birds were more involved in local processes. We would expect that species' roles in the metanetwork will translate into different conservation values for maintaining functioning of seed-dispersal networks.</p>
Fluorescence Microscopy Data for Cellular Detection using Object Detection Networks.
<p>This data accompanies work from the paper entitled: </p> <p><strong>Object Detection Networks and Augmented Reality for Cellular Detection in Fluorescence Microscopy Acquisition and Analysis. </strong></p> <p>Waithe D1*,2,, Brown JM3, Reglinski K4,6,7, Diez-Sevilla I<sup>5</sup>, Roberts D<sup>5</sup>, Christian Eggeling1,4,6,8</p> <p>1 Wolfson Imaging Centre Oxford and 2 MRC WIMM Centre for Computational Biology and 3 MRC Molecular Haematology Unit and 4 MRC Human Immunology Unit, Weatherall Institute of Molecular Medicine, University of Oxford, OX3 9DS, Oxford, United Kingdom. 5 Nuffield Division of Clinical Laboratory Sciences, Radcliffe Department of Medicine, John Radcliffe Hospital, University of Oxford, Headley Way, Oxford, OX3 9DU.<br> 6 Institute of Applied Optics and Biophysics, Friedrich-Schiller-University Jena, Max-Wien Platz 4, 07743 Jena, Germany.<br> 7 University Hospital Jena (UKJ), Bachstraße 18, 07743 Jena, Germany.<br> 8 Leibniz Institute of Photonic Technology e.V., Albert-Einstein-Straße 9, 07745 Jena, Germany.</p> <p>Further details of these datasets can be found in the methods section of the above paper.</p> <p><strong>Erythroblast DAPI (+glycophorin A):</strong> erythroblast cells were stained with DAPI and for glycophorin A protein (CD235a antibody, JC159 clone, Dako) and with Alexa Fluor 488 secondary antibody (Invitrogen). DAPI staining was performed through using VectaShield Hard Set mounting solution with DAPI (Vector Lab). Num. of images used for training: 80 and testing: 80. Average number of cells per image: 4.5.</p> <p><strong>Neuroblastoma phalloidin (+DAPI): </strong>images of neuroblastoma cells (N1E115) stained with phalloidin and DAPI were acquired from the Cell Image Library [26]. Cell images in the original dataset were acquired with a larger field of view than our system and so we divided each image into four sub-images and also created ROI bounding boxes for each of the cells in the image. The images were stained for FITC-phalloidin and DAPI. Num. of images used for training: 180, testing: 180. Average number of cells per image: 11.7.</p> <p><strong>Fibroblast nucleopore</strong>: fibroblast (GM5756T) cells were stained for a nucleopore protein (anti-Nup153 mouse antibody, Abcam) and detected with anti-mouse Alexa Fluor 488. Num. of images for training: 26 and testing: 20. Average number of cells per image: 4.8.</p> <p><strong>Eukaryote DAPI:</strong> eukaryote cells were stained with DAPI and fixed and mounted in Vectashield (Vector Lab). Num. of images for training: 40 and testing: 40. Average number of cells per image: 8.9.</p> <p><strong>C127 DAPI:</strong> C127 cells were initially treated with a technique called RASER-FISH[27], stained with DAPI and fixed and mounted in Vectashield (Vector Lab). Num. of images for training: 30 and testing: 30. Average number of cells per image: 7.1.</p> <p><strong>HEK peroxisome All</strong>: HEK-293 cells expressing peroxisome-localized GFP-SCP2 protein. Cells were transfected with GFP-SCP2 protein, which contains the PTS-1 localization signal, which redirects the fluorescently tagged protein to the actively importing peroxisomes[28]. Cells were fixed and mounted. Num. of images for training: 55 and testing: 55. Additionally we sub-categorised the cells as ‘punctuate’ and ‘non-punctuate’, where ‘punctuate’ would represent cells that have staining where the peroxisomes are discretely visible and ‘non-punctuate’ would be diffuse staining within the cell. The ‘HEK peroxisome All’ dataset contains ROI for all the cells: average number of cells per image: 7.9. The ‘HEK peroxisome’ dataset contains only those cells with punctuate fluorescence: average number of punctuate cells per image: 3.9.</p> <p><strong>Erythroid DAPI All: </strong>Murine embryoid body-derived erythroid cells, differentiated from mES cells. Stained with DAPI and fixed and mounted in Vectashield (Vector Lab). Num. of images for training: 51 and testing: 50. Multinucleate cells are seen with this differentiation procedure. There is a variation in size of the nuclei (nuclei become smaller as differentiation proceeds). The smaller, 'late erythroid' nuclei contain heavily condensed DNA and often have heavy ‘blobs’ of heterochromatin visible. Apoptopic cells are also present, with apoptotic bodies clearly present. The ‘Erythroid DAPI All’ dataset contains ROI for all the cells in the image. Average number of cells per image: 21.5. The subset ‘Erythroid DAPI’ contains non-apoptotic cells only: average number of cells per image: 11.9</p> <p><strong>COS-7 nucleopore. </strong>Slides were acquired from GATTAquant. GATTA-Cells 1C are single color COS-7 cells stained for Nuclear pore complexes (Anti-Nup) and with Alexa Fluor 555 Fab(ab’)2 secondary stain. GATTA-Cells are embedded in ProLong Diamond. Num. of images for training: 50 and testing: 50. Average number of cells per image: 13.2</p> <p><strong>COS-7 nucleopore 40x</strong>. Same GATTA-Cells 1C slides (GATTAquant) as above but imaged on Nikon microscope, with 40x NA 0.6 objective. Num. of images for testing: 11. Average number of cells per image: 31.6.</p> <p><strong>COS-7 nucleopore 10x.</strong> Same GATTA-Cells 1C slides (GATTAquant) as above but imaged on Nikon microscope, with 10x NA 0.25 objective. Num. of images for testing: 20. Average number of cells per image: 24.6</p> <p><strong>Dataset Annotation</strong></p> <p>Datasets were annotated by a skilled user. These annotations represent the ground-truth of each image with bounding boxes (regions) drawn around each cell present within the staining. Annotations were produced using Fiji/ImageJ [29] ROI Manager and also through using the OMERO [30] ROI drawing interface (<a href="https://www.openmicroscopy.org/omero/">https://www.openmicroscopy.org/omero/</a>). The dataset labels were then converted into a format compatible with Faster-RCNN (Pascal), YOLOv2, YOLOv3 and also RetinaNet. The scripts used to perform this conversion are documented in the repository (<a href="https://github.com/dwaithe/amca">https://github.com/dwaithe/amca</a>/scripts/).</p>
ScienceDex guides
Understand access before you commit
These curated guides explain access requirements, typical timelines, costs, and reuse considerations for widely used research datasets.
Allen Brain Atlas
Allen Brain Atlas is an Allen Institute collection of brain map atlases, datasets, APIs, and analysis tools covering mouse, human, and non-human primate brain resources.
Annotated Behaviour and Observability Dataset (ABODe)
ABODe is a University of Edinburgh DataShare dataset for behavior classification in group-housed mice using home-cage video, identities, bounding boxes, ground-plate positions, and annotator labels.
DANDI Archive for NWB datasets
DANDI is a BRAIN Initiative archive for publishing and sharing neurophysiology data, including electrophysiology, optophysiology, and behavioral data packaged as NWB and related standards.
International Brain Laboratory public data
The International Brain Laboratory public data releases expose standardized mouse decision-making experiments, including Neuropixels recordings, widefield calcium imaging, behavior, and session metadata accessed through the ONE API.
OpenNeuro
OpenNeuro is a free, open platform for sharing neuroimaging datasets, with public search, dataset pages, and download paths for web, S3, DataLad, and the OpenNeuro CLI.